Hinge action versus grip in translocation by RNA polymerase.
作者： Yuri A. Nedialkov , Kristopher Opron , Hailey L. Caudill , Fadi Assaf , Amanda J. Anderson
DOI: 10.1080/21541264.2017.1330179
关键词: Biophysics 、 Chromosomal translocation 、 Active site 、 RNA 、 Threading (protein sequence) 、 Exonuclease III 、 Crystallography 、 Elongation 、 Biology 、 RNA polymerase 、 Hinge
摘要: ABSTRACTBased on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In simulation of ternary elongation complex, the clamp downstream cleft were observed to close. Hinges within bridge helix trigger loop supported generation force against RNA–DNA hybrid resulting in opening furthest upstream i−8 bp, establishing conditions RNAP sliding. The β flap tip most N-terminal β′ Zn finger engage RNA, indicating path threading out exit channel. Because connects active site through subunit double-Ψ–β-barrel associated sandwich barrel motif (also called domain), coupled channel RNA–DNA. Using an exonuclease III assay monitor complexes, we show that K+ Mg2+ also 3′...
sci-hub.se 参考文章(30)
Lakshminarayan M Iyer, Eugene V Koonin, L Aravind, Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC Structural Biology. ,vol. 3, pp. 1- 23 ,(2003) , 10.1186/1472-6807-3-1
Shun-ichi Sekine, Yuko Murayama, Vladimir Svetlov, Evgeny Nudler, Shigeyuki Yokoyama, Ratcheting of RNA polymerase toward structural principles of RNA polymerase operations. Transcription. ,vol. 6, pp. 56- 60 ,(2015) , 10.1080/21541264.2015.1059922
Milija Jovanovic, Patricia C Burrows, Daniel Bose, Beatriz Cámara, Simone Wiesler, Xiaodong Zhang, Sivaramesh Wigneshweraraj, Robert OJ Weinzierl, Martin Buck, None, Activity Map of the Escherichia coli RNA Polymerase Bridge Helix Journal of Biological Chemistry. ,vol. 286, pp. 14469- 14479 ,(2011) , 10.1074/JBC.M110.212902
Maria Kireeva, Mikhail Kashlev, Zachary F. Burton, Translocation by multi-subunit RNA polymerases Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. ,vol. 1799, pp. 389- 401 ,(2010) , 10.1016/J.BBAGRM.2010.01.007
D.-A. Silva, D. R. Weiss, F. Pardo Avila, L.-T. Da, M. Levitt, D. Wang, X. Huang, Millisecond dynamics of RNA polymerase II translocation at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, pp. 7665- 7670 ,(2014) , 10.1073/PNAS.1315751111
Yuri A. Nedialkov, Kristopher Opron, Fadi Assaf, Irina Artsimovitch, Maria L. Kireeva, Mikhail Kashlev, Robert I. Cukier, Evgeny Nudler, Zachary F. Burton, The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. ,vol. 1829, pp. 187- 198 ,(2013) , 10.1016/J.BBAGRM.2012.11.005
Yuri A. Nedialkov, Zachary F. Burton, Translocation and fidelity ofEscherichia coliRNA polymerase Transcription. ,vol. 4, pp. 136- 143 ,(2013) , 10.4161/TRNS.25527
Yuri A. Nedialkov, Evgeny Nudler, Zachary F. Burton, RNA polymerase stalls in a post-translocated register and can hyper-translocate. Transcription. ,vol. 3, pp. 260- 269 ,(2012) , 10.4161/TRNS.22307
Maria L Kireeva, Kristopher Opron, Steve A Seibold, Céline Domecq, Robert I Cukier, Benoit Coulombe, Mikhail Kashlev, Zachary F Burton, Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase BMC Biophysics. ,vol. 5, pp. 11- 11 ,(2012) , 10.1186/2046-1682-5-11
Steve A. Seibold, Badri Nath Singh, Chunfen Zhang, Maria Kireeva, Céline Domecq, Annie Bouchard, Anthony M. Nazione, Michael Feig, Robert I. Cukier, Benoit Coulombe, Mikhail Kashlev, Michael Hampsey, Zachary F. Burton, Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. ,vol. 1799, pp. 575- 587 ,(2010) , 10.1016/J.BBAGRM.2010.05.002